I just don't see how they're going to get away from military. If N7 still remains wherever/whenever they are, then the Alliance still remains. Maybe we'll start at the N6 level, working toward our N7 designation. Maybe instead of being in charge of a group of people, like Shepard, you'll be working under a captain for a change. What would it be like to work for Shepard instead of being Shepard? For all we know, we could start out like good ol' Corporal Jenkins.
Yeah, the insistence on N7 (for clear branding and marketing) could be a bit of a handcuff. It can be circumvented, I guess. You could be Alliance protection for an expedition into the unknown. When the expedition gets stranded in an unknown sector of space, past affiliations mean less. It isn't relevant that you're Alliance, but only that you are willing and capable of getting the crew home. That's one idea.
As to the pirate angle many are suggesting, I'd not really want to see that. I don't want to play a bad guy. Smugglers, like Malcolm Reynolds and crew, would be okay. Smugglers are sneaky, rather than overtly evil and violent. Pirates are violent criminals. I'd prefer to not play that type of character in a Mass Effect game. I enjoyed AC Black Flag, but I never expect to play a good guy in AC games, especially that one. (I always laugh at the end when Anne says to Edward: "You're a good man, Edward". Yeah, right. I've killed hundreds for greed alone.) I'm not yet ready to stop playing the good-guy hero in this series.